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- PDB-1mfs: DYNAMICAL BEHAVIOR OF THE HIV-1 NUCLEOCAPSID PROTEIN; NMR, 30 STR... -

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Basic information

Entry
Database: PDB / ID: 1mfs
TitleDYNAMICAL BEHAVIOR OF THE HIV-1 NUCLEOCAPSID PROTEIN; NMR, 30 STRUCTURES
ComponentsHIV-1 NUCLEOCAPSID PROTEIN
KeywordsVIRAL PROTEIN / NUCLEOCAPSID PROTEIN / DYNAMICS / ZINC KNUCKLE / HIV-1 / ZINC BINDING
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / structural molecule activity / host cell plasma membrane / virion membrane / proteolysis / DNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain ...Zinc finger, CCHC-type / HIV-1 Nucleocapsid Protein / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Few Secondary Structures / Irregular / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus
MethodSOLUTION NMR / distance geometry
AuthorsSummers, M.F. / Turner, B.G. / De Guzman, R.N. / Lee, B.M. / Tjandra, N.
CitationJournal: J.Mol.Biol. / Year: 1998
Title: Dynamical behavior of the HIV-1 nucleocapsid protein.
Authors: Lee, B.M. / De Guzman, R.N. / Turner, B.G. / Tjandra, N. / Summers, M.F.
History
DepositionApr 1, 1998Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 NUCLEOCAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5173
Polymers6,3861
Non-polymers1312
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)30 / 30LEAST RESTRAINT VIOLATION
Representative

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Components

#1: Protein HIV-1 NUCLEOCAPSID PROTEIN


Mass: 6386.495 Da / Num. of mol.: 1 / Fragment: NUCLEOCAPSID, ZINC BINDING DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Genus: Lentivirus / Strain: NL4-3 / Cell line: BL21 / Gene: NC / Plasmid: PET-3A / Gene (production host): NC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSE / References: UniProt: P35963
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121TOCSY
131HSQC
141HMQC
1513D NOESY-HSQC
1613D TOCSY-HSQC
1713D HMQC-NOESY
1814D CNNOE

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Sample preparation

Sample conditionspH: 6.5 / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker BRUKER DMXBrukerBRUKER DMX6001
GE GE OMEGAGEGE OMEGA6002

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Processing

NMR software
NameVersionDeveloperClassification
DIANA2.8WUTHRICHrefinement
DIANAstructure solution
RefinementMethod: distance geometry / Software ordinal: 1
Details: DETAILS OF THE REFINEMENT AND STRATEGY ARE LOCATED IN THE PUBLICATION
NMR ensembleConformer selection criteria: LEAST RESTRAINT VIOLATION / Conformers calculated total number: 30 / Conformers submitted total number: 30

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